Horses in Pre-Columbian America

by Brian Dunning
June 29, 2021

Today we're going to point the skeptical eye at a hot topic in conservation: the history of the wild horse in America. The science indicates that after originating in America, horses went extinct on the continent with many other species of megafauna at the end of the last ice age, but a growing movement of various groups in the United States seeks to overturn this body of knowledge with the seemingly random claim that horses were never extinct here after all. Why? We're going to find out.

According to all the fossil and genetic evidence, ancient horses evolved in the Americas, eventually producing the genus Equus, which includes all modern equines. 2-3 million years ago, they crossed the Bering Land Bridge and spread throughout Eurasia. Several extinctions occurred in America, each time being repopulated by horses coming back over from Asia; but by the time of the last extinction some 11 to 13 thousand years ago, the Bering Land Bridge was no more, the resupply channel was cut off, and horses were extinct in America for good.

Fast forward to the 1500s, when Spanish conquerors following in the footsteps of Columbus brought horses back, first to the Caribbean where their numbers were multiplied on vast ranches, and finally to Mexico. This began a constant leakage of stolen and escaped horses to the Native Americans. Many Native Americans were employed as vaqueros on Spanish ranches in the American southwest, and together with a number of large-scale raids of such ranches, the horse rapidly spread across all North American plains tribes. The horse revolutionized their ability to hunt, to travel, to trade, and to wage war; and the significance of the resulting symbiosis between Native Americans and their horses cannot be overstated.

But now, quite suddenly, this history is being called into question by some who say the horse was never extinct in America. There are basically three groups promoting this, and it's a virtual guarantee that any published research you find that makes this claim was written by someone representing one or more of these groups. The first consist of Native American groups. Certainly not all Native Americans are on this bandwagon, but those who are generally come from the perspective that the histories of the horse and of Native Americans are deeply intertwined and they take some affront at the notion that European invaders should be due any credit for what was such an immense leap of progress for their ancestors. The evidence they present is mainly in the form of oral histories from various tribes. The second group of advocates are scholars working on behalf of the Church of Jesus Christ of Latter-Day Saints (the Mormons), who have long argued in favor of certain alternative histories in the hope of bolstering recognition of their Book of Mormon as a factual historical document. The Book of Mormon is full of horses in the Americas during Biblical times — a clear impossibility; this fatal error having been made because it was written during the 1800s by people who had no knowledge of equine history.

The third group of proponents are the ones who have brought this question into today's headlines, and they are the wild horse conservationists. For a long time, conservationists have butted heads with the US Bureau of Land Management (BLM), which manages wild horse herds. We're not going to go into the details of wild horse management today because it's a separate subject, but the relevant details are that the conservationists believe the BLM understates the population decline of wild herds and seek to have them declared threatened or endangered, which would increase their protections. To receive this status, an animal typically must be a native species. Non-native or re-introduced species, like horses, typically wouldn't qualify for these protections. So there's a powerful motivation for conservationists to embrace — and even publish — research claiming horses never went extinct in the Americas.

Together, these three groups comprise a formidable press release machine. But representing the side of science, nobody publishes science that merely confirms what we've already known for a long time; so the unscientific perspective is going essentially unchallenged in the popular media. If you or someone you know has heard in the past few years that new research shows horses never went extinct in the Americas, you were probably given no reason to doubt it. But it is false, and now we'll talk about the important half of that question, which is how we know that it's false.

The end of the Pleistocene epoch brought the extinction of many, many North American megafauna besides just the horse: the woolly mammoth, American camels, dire wolves, short-faced bears, sabre-toothed cats, the stag-moose, woolly rhinos and giant ground sloths are the other familiar examples. Hunting by humans played a role in these extinctions — horse and camel proteins have been found on 13,000-year-old butchering tools made by the big game hunting Clovis culture in what is today Boulder, Colorado. Another reason for the extinctions was climate; the Younger-Dryas period was a 1,200-year interruption to the gradual climatic warming ever since the recession of ice from the most recent ice age began. This brought massive changes to vegetation, and a leading theory is that the resulting grittier grass, high in silica, was too abrasive for horse teeth. But regardless, we don't have the complete picture for the reason for these extinctions; only that they did happen.

A clear photograph of the extinctions is best provided in the permafrost of North America. Prior to 12,000 years ago (give or take), the soil is rich with proteins and other biochemical evidence of horses and all those other species of megafauna. But after the extinction, horses are just as absent from that entire record as are the others. Analysis continues — it is in fact an active area of research — and occasionally samples are found that push those boundaries. It is entirely possible that it will eventually be more thoroughly evidenced that horses did persist for a few thousand years later than previously known, as some fringe evidence does indicate; but that day is not yet today.

And moreover, we have the historical fact of the mass importation programs run by the Spanish and other later Europeans, who created vast ranches on which to multiply thousands of imported horses — a task which would not have been needed if horses were already here. They could have simply bred native horses into the numbers they needed, much cheaper, easier, and faster.

The Spanish went to great lengths to keep the horses out of Native American hands, but seeing their value, the natives stepped up their efforts to acquire them. One particularly bloody event in what is now Santa Fe, New Mexico, took place in 1680 and is called the Pueblo Revolt. Popé, a Pueblo religious leader, led an assault that left 400 Spanish dead and transferred 1,500 horses into Native American hands, the largest single transfer known. These were traded to other tribes and they spread rapidly across North America. It is hard to reconcile such events with the Native Americans already having horses of their own.

One of the horses my daughter Erika owns is a mustang named Terra. Terra was raised wild in the Warm Springs herd in Oregon. She can't be ridden so she lives here on our property as a pasture horse. In preparation for this episode, Erika and I thought it would be fun to do a genetic test to learn Terra's ancestry. So Erika plucked a few dozen hairs from her mane and mailed them with the fee to the Texas A&M Animal Genetics Laboratory. Going by Terra's appearance, Erika bet she'd come back as mostly Thoroughbred and Quarter Horse.

Although this sounds like a single anecdotal data point, it's not really; like all mustangs, the Warm Springs herd is interbred, so a sample from one is really a sample from all. And such a herd from the Pacific Northwest is really the most important one to sample for the question we're trying to answer today, as the Pacific Northwest is geographically farthest from where Europeans introduced horses to the Americas in the 16th century. If there had been an indigenous horse population in North America, Pacific Northwest mustangs would be the ones most likely to retain that original genetic fingerprint, and least likely to have been contaminated by the European breeds.

Erika turned out to have called Terra's ancestry right on the nose. DNA results are given as the top three breeds most likely to be ancestors of the subject horse. Terra is #1 Thoroughbred; #2 Quarter Horse; and #3 Trakehner. All three breeds are closely related phylogenetically. The Trakehner is most interesting. This breed is descended from Middle Ages cavalry horses, with some Arabian influence; giving Terra's ancestry a clear anchor in Europe. Thoroughbreds and Quarter Horses are more recent. Thoroughbreds were created in England around 1700 from a group of known foundation sires, mostly successful Arabian racing horses. American colonists created Quarter Horses around 1750 from a handful of imported Thoroughbreds, selectively bred with other horses. One of these imported Thoroughbred sires was a famous one named Janus, who was the grandson of Godolphin Arabian, himself a foundation sire of Thoroughbreds.

Unsurprisingly, Terra — like all Warm Springs mustangs, and like all American wild horses — has the genetic markers of exclusively European ancestry. No mythical "indigenous American horse" was listed in her results. However, this is because the test only looks for the markers it's designed to look for. If the indigenous breed were to exist but was not in Texas A&M's database, Terra could be 99% indigenous but the test would have still come back showing only the recognized markers from Thoroughbred, Quarter Horse, and Trakehner.

So that raises the question: How do we know the Texas A&M database is complete? Well, it's not; they say so. They exclude certain rare or endangered breeds that are unlikely to be ancestors of a North American subject horse, such as the Timor pony from Timor Island, the Cheju horse from Korea, the Namib horse from Africa, and others. What they do include are the 50 breeds representing the most common ancestors of countless horses tested throughout North America.

For there to have been an indigenous American breed, it would mean that all genetic traces of its existence have vanished, totally replaced in just a few hundred years by a relatively tiny imported population. Given this evidence, there's simply no room for the indigenous horse conjecture to be correct. When we can go back through Terra's genes and find a single foundation sire like Janus, it's simply not mathematically plausible for the genes of an entire continent's founding population — genetically distinct from all European breeds — to have completely vanished from the genomes of all the horses ever sequenced by Texas A&M. The explanation, of course, is that there never was such an indigenous population.

Genetic studies of horses have included the last survivors in the Americas, called the Yukon horse — the very last to die out at the extinction. Remains recovered from the Alaskan permafrost allowed genetic analysis to be done, just as we've done with woolly mammoths. The Yukon horse was found to be genetically equivalent to the modern horse — but obviously lacking any of the markers of modern breeds.

The problem of federal protection for wild horses as a native species can easily be resolved without resorting to false histories. A native species is one that originated there and that coevolved with its habitat. Although the horse took a break, it did indeed do both of these things: It originated in North America, and it evolved with its habitat. This renders the question of whether it's a native species purely an issue of semantics, not of science. Any reasonable analysis shows that the horse is genetically identical to how it would be if it had not taken that break, and its habitat is exactly as it was before it went extinct. There are two things that we should do to resolve the question of the history of the horse: first, extend it all the protections it is entitled to as a native species; and second, stop inventing false, unscientific histories to try and force this decision to be made for the wrong reason. It is only when we build our puzzle from pieces consisting of true science and true history that we get a truly complete picture that withstands all scrutiny.

Correction: An earlier version of this incorrectly referred to the Pleistocene epoch as the Pleistocene era. —BD

By Brian Dunning
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